-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.util.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.util.Format;\r
-\r
-/**\r
- * Parse and create Jalview Features files Detects GFF format features files and\r
- * parses. Does not implement standard print() - call specific printFeatures or\r
- * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object\r
- * for the features annotation - this normally works on an exact match.\r
- * \r
- * @author AMW\r
- * @version $Revision$\r
- */\r
-public class FeaturesFile extends AlignFile\r
-{\r
- /**\r
- * work around for GFF interpretation bug where source string becomes\r
- * description rather than a group\r
- */\r
- private boolean doGffSource = true;\r
-\r
- /**\r
- * Creates a new FeaturesFile object.\r
- */\r
- public FeaturesFile()\r
- {\r
- }\r
-\r
- /**\r
- * Creates a new FeaturesFile object.\r
- * \r
- * @param inFile\r
- * DOCUMENT ME!\r
- * @param type\r
- * DOCUMENT ME!\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public FeaturesFile(String inFile, String type) throws IOException\r
- {\r
- super(inFile, type);\r
- }\r
-\r
- public FeaturesFile(FileParse source) throws IOException\r
- {\r
- super(source);\r
- }\r
-\r
- /**\r
- * The Application can render HTML, but the applet will remove HTML tags and\r
- * replace links with %LINK% Both need to read links in HTML however\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align, Hashtable colours,\r
- boolean removeHTML)\r
- {\r
- return parse(align, colours, null, removeHTML);\r
- }\r
-\r
- /**\r
- * The Application can render HTML, but the applet will remove HTML tags and\r
- * replace links with %LINK% Both need to read links in HTML however\r
- * \r
- * @throws IOException\r
- * DOCUMENT ME!\r
- */\r
- public boolean parse(AlignmentI align, Hashtable colours,\r
- Hashtable featureLink, boolean removeHTML)\r
- {\r
- String line = null;\r
- try\r
- {\r
- SequenceI seq = null;\r
- String type, desc, token = null;\r
-\r
- int index, start, end;\r
- float score;\r
- StringTokenizer st;\r
- SequenceFeature sf;\r
- String featureGroup = null, groupLink = null;\r
- Hashtable typeLink = new Hashtable();\r
-\r
- boolean GFFFile = true;\r
-\r
- while ((line = nextLine()) != null)\r
- {\r
- if (line.startsWith("#"))\r
- {\r
- continue;\r
- }\r
-\r
- st = new StringTokenizer(line, "\t");\r
- if (st.countTokens() > 1 && st.countTokens() < 4)\r
- {\r
- GFFFile = false;\r
- type = st.nextToken();\r
- if (type.equalsIgnoreCase("startgroup"))\r
- {\r
- featureGroup = st.nextToken();\r
- if (st.hasMoreElements())\r
- {\r
- groupLink = st.nextToken();\r
- featureLink.put(featureGroup, groupLink);\r
- }\r
- }\r
- else if (type.equalsIgnoreCase("endgroup"))\r
- {\r
- // We should check whether this is the current group,\r
- // but at present theres no way of showing more than 1 group\r
- st.nextToken();\r
- featureGroup = null;\r
- groupLink = null;\r
- }\r
- else\r
- {\r
- Object colour = null;\r
- String colscheme = st.nextToken();\r
- if (colscheme.indexOf("|") > -1)\r
- {\r
- // Parse '|' separated graduated colourscheme fields:\r
- // mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue\r
- // first four are required.\r
- // first two are hexadecimal or word equivalent colours.\r
- // second two are values parsed as floats.\r
- // fifth is either 'above','below', or 'none'.\r
- // sixth is a float value and only required when fifth is either\r
- // 'above' or 'below'.\r
- StringTokenizer gcol = new StringTokenizer(colscheme, "|");\r
- String mincol = gcol.nextToken(), maxcol = gcol.nextToken();\r
- String abso = gcol\r
- .nextToken(), minval, maxval;\r
- if (abso.toLowerCase().indexOf("abso")!=0) {\r
- minval = abso;\r
- abso = null;\r
- } else {\r
- minval = gcol.nextToken();\r
- }\r
- maxval = gcol.nextToken();\r
- // set defaults\r
- int threshtype = AnnotationColourGradient.NO_THRESHOLD;\r
- float min=Float.MIN_VALUE,max=Float.MAX_VALUE,threshval=Float.NaN;\r
- try\r
- {\r
- if (minval.length()>0) { \r
- min = new Float(minval).floatValue();\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Couldn't parse the minimum value for graduated colour for type ("\r
- + colscheme + ") - did you misspell 'auto' for the optional automatic colour switch ?");\r
- e.printStackTrace();\r
- }\r
- try\r
- {\r
- if (maxval.length()>0) { \r
- max = new Float(maxval).floatValue();\r
- }\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Couldn't parse the maximum value for graduated colour for type ("\r
- + colscheme + ")");\r
- e.printStackTrace();\r
- }\r
- try\r
- {\r
- colour = new jalview.schemes.GraduatedColor(\r
- new UserColourScheme(mincol).findColour('A'),\r
- new UserColourScheme(maxcol).findColour('A'),\r
- min, max);\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Couldn't parse the graduated colour scheme ("\r
- + colscheme + ")");\r
- e.printStackTrace();\r
- }\r
- if (colour != null)\r
- {\r
- ((jalview.schemes.GraduatedColor)colour).setAutoScaled(abso==null);\r
- // add in any additional parameters\r
- String ttype = null, tval = null;\r
- if (gcol.hasMoreTokens())\r
- {\r
- // threshold type and possibly a threshold value\r
- ttype = gcol.nextToken();\r
- if (ttype.toLowerCase().startsWith("below"))\r
- {\r
- ((jalview.schemes.GraduatedColor) colour)\r
- .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);\r
- }\r
- else if (ttype.toLowerCase().startsWith("above"))\r
- {\r
- ((jalview.schemes.GraduatedColor) colour)\r
- .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);\r
- }\r
- else\r
- {\r
- ((jalview.schemes.GraduatedColor) colour)\r
- .setThreshType(AnnotationColourGradient.NO_THRESHOLD);\r
- if (!ttype.toLowerCase().startsWith("no"))\r
- {\r
- System.err\r
- .println("Ignoring unrecognised threshold type : "\r
- + ttype);\r
- }\r
- }\r
- }\r
- if (((GraduatedColor)colour).getThreshType()!=AnnotationColourGradient.NO_THRESHOLD)\r
- {\r
- tval = gcol.nextToken();\r
- try\r
- {\r
- ((jalview.schemes.GraduatedColor) colour)\r
- .setThresh(new Float(tval).floatValue());\r
- } catch (Exception e)\r
- {\r
- System.err\r
- .println("Couldn't parse threshold value as a float: ("\r
- + tval + ")");\r
- e.printStackTrace();\r
- }\r
- }\r
- // parse the thresh-is-min token ?\r
- if (gcol.hasMoreTokens())\r
- {\r
- System.err\r
- .println("Ignoring additional tokens in parameters in graduated colour specification\n");\r
- while (gcol.hasMoreTokens())\r
- {\r
- System.err.println("|" + gcol);\r
- }\r
- System.err.println("\n");\r
- }\r
- }\r
- }\r
- else\r
- {\r
- UserColourScheme ucs = new UserColourScheme(colscheme);\r
- colour = ucs.findColour('A');\r
- }\r
- if (colour != null)\r
- {\r
- colours.put(type, colour);\r
- }\r
- if (st.hasMoreElements())\r
- {\r
- String link = st.nextToken();\r
- typeLink.put(type, link);\r
- if (featureLink == null)\r
- {\r
- featureLink = new Hashtable();\r
- }\r
- featureLink.put(type, link);\r
- }\r
- }\r
- continue;\r
- }\r
- String seqId = "";\r
- while (st.hasMoreElements())\r
- {\r
-\r
- if (GFFFile)\r
- {\r
- // Still possible this is an old Jalview file,\r
- // which does not have type colours at the beginning\r
- seqId = token = st.nextToken();\r
- seq = align.findName(seqId, true);\r
- if (seq != null)\r
- {\r
- desc = st.nextToken();\r
- String group = null;\r
- if (doGffSource && desc.indexOf(' ') == -1)\r
- {\r
- // could also be a source term rather than description line\r
- group = new String(desc);\r
- }\r
- type = st.nextToken();\r
- try\r
- {\r
- String stt = st.nextToken();\r
- if (stt.length() == 0 || stt.equals("-"))\r
- {\r
- start = 0;\r
- }\r
- else\r
- {\r
- start = Integer.parseInt(stt);\r
- }\r
- } catch (NumberFormatException ex)\r
- {\r
- start = 0;\r
- }\r
- try\r
- {\r
- String stt = st.nextToken();\r
- if (stt.length() == 0 || stt.equals("-"))\r
- {\r
- end = 0;\r
- }\r
- else\r
- {\r
- end = Integer.parseInt(stt);\r
- }\r
- } catch (NumberFormatException ex)\r
- {\r
- end = 0;\r
- }\r
- // TODO: decide if non positional feature assertion for input data\r
- // where end==0 is generally valid\r
- if (end == 0)\r
- {\r
- // treat as non-positional feature, regardless.\r
- start = 0;\r
- }\r
- try\r
- {\r
- score = new Float(st.nextToken()).floatValue();\r
- } catch (NumberFormatException ex)\r
- {\r
- score = 0;\r
- }\r
-\r
- sf = new SequenceFeature(type, desc, start, end, score, group);\r
-\r
- try\r
- {\r
- sf.setValue("STRAND", st.nextToken());\r
- sf.setValue("FRAME", st.nextToken());\r
- } catch (Exception ex)\r
- {\r
- }\r
-\r
- if (st.hasMoreTokens())\r
- {\r
- StringBuffer attributes = new StringBuffer();\r
- while (st.hasMoreTokens())\r
- {\r
- attributes.append("\t" + st.nextElement());\r
- }\r
- // TODO validate and split GFF2 attributes field ? parse out\r
- // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as\r
- // sf.setValue(attrib, val);\r
- sf.setValue("ATTRIBUTES", attributes.toString());\r
- }\r
-\r
- seq.addSequenceFeature(sf);\r
- while ((seq = align.findName(seq, seqId, true)) != null)\r
- {\r
- seq.addSequenceFeature(new SequenceFeature(sf));\r
- }\r
- break;\r
- }\r
- }\r
-\r
- if (GFFFile && seq == null)\r
- {\r
- desc = token;\r
- }\r
- else\r
- {\r
- desc = st.nextToken();\r
- }\r
- if (!st.hasMoreTokens())\r
- {\r
- System.err\r
- .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");\r
- // in all probability, this isn't a file we understand, so bail\r
- // quietly.\r
- return false;\r
- }\r
-\r
- token = st.nextToken();\r
-\r
- if (!token.equals("ID_NOT_SPECIFIED"))\r
- {\r
- seq = align.findName(seqId = token, true);\r
- st.nextToken();\r
- }\r
- else\r
- {\r
- seqId = null;\r
- try\r
- {\r
- index = Integer.parseInt(st.nextToken());\r
- seq = align.getSequenceAt(index);\r
- } catch (NumberFormatException ex)\r
- {\r
- seq = null;\r
- }\r
- }\r
-\r
- if (seq == null)\r
- {\r
- System.out.println("Sequence not found: " + line);\r
- break;\r
- }\r
-\r
- start = Integer.parseInt(st.nextToken());\r
- end = Integer.parseInt(st.nextToken());\r
-\r
- type = st.nextToken();\r
-\r
- if (!colours.containsKey(type))\r
- {\r
- // Probably the old style groups file\r
- UserColourScheme ucs = new UserColourScheme(type);\r
- colours.put(type, ucs.findColour('A'));\r
- }\r
- sf = new SequenceFeature(type, desc, "", start, end, featureGroup);\r
- if (st.hasMoreTokens())\r
- {\r
- try\r
- {\r
- score = new Float(st.nextToken()).floatValue();\r
- // update colourgradient bounds if allowed to \r
- } catch (NumberFormatException ex)\r
- {\r
- score = 0;\r
- }\r
- sf.setScore(score);\r
- }\r
- if (groupLink != null && removeHTML)\r
- {\r
- sf.addLink(groupLink);\r
- sf.description += "%LINK%";\r
- }\r
- if (typeLink.containsKey(type) && removeHTML)\r
- {\r
- sf.addLink(typeLink.get(type).toString());\r
- sf.description += "%LINK%";\r
- }\r
-\r
- parseDescriptionHTML(sf, removeHTML);\r
-\r
- seq.addSequenceFeature(sf);\r
-\r
- while (seqId != null\r
- && (seq = align.findName(seq, seqId, false)) != null)\r
- {\r
- seq.addSequenceFeature(new SequenceFeature(sf));\r
- }\r
- // If we got here, its not a GFFFile\r
- GFFFile = false;\r
- }\r
- }\r
- } catch (Exception ex)\r
- {\r
- System.out.println(line);\r
- System.out.println("Error parsing feature file: " + ex + "\n" + line);\r
- ex.printStackTrace(System.err);\r
- return false;\r
- }\r
-\r
- return true;\r
- }\r
-\r
- public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)\r
- {\r
- if (sf.getDescription() == null)\r
- {\r
- return;\r
- }\r
-\r
- if (removeHTML\r
- && sf.getDescription().toUpperCase().indexOf("<HTML>") == -1)\r
- {\r
- removeHTML = false;\r
- }\r
-\r
- StringBuffer sb = new StringBuffer();\r
- StringTokenizer st = new StringTokenizer(sf.getDescription(), "<");\r
- String token, link;\r
- int startTag;\r
- String tag = null;\r
- while (st.hasMoreElements())\r
- {\r
- token = st.nextToken("&>");\r
- if (token.equalsIgnoreCase("html") || token.startsWith("/"))\r
- {\r
- continue;\r
- }\r
-\r
- tag = null;\r
- startTag = token.indexOf("<");\r
-\r
- if (startTag > -1)\r
- {\r
- tag = token.substring(startTag + 1);\r
- token = token.substring(0, startTag);\r
- }\r
-\r
- if (tag != null && tag.toUpperCase().startsWith("A HREF="))\r
- {\r
- if (token.length() > 0)\r
- {\r
- sb.append(token);\r
- }\r
- link = tag.substring(tag.indexOf("\"") + 1, tag.length() - 1);\r
- String label = st.nextToken("<>");\r
- sf.addLink(label + "|" + link);\r
- sb.append(label + "%LINK%");\r
- }\r
- else if (tag != null && tag.equalsIgnoreCase("br"))\r
- {\r
- sb.append("\n");\r
- }\r
- else if (token.startsWith("lt;"))\r
- {\r
- sb.append("<" + token.substring(3));\r
- }\r
- else if (token.startsWith("gt;"))\r
- {\r
- sb.append(">" + token.substring(3));\r
- }\r
- else if (token.startsWith("amp;"))\r
- {\r
- sb.append("&" + token.substring(4));\r
- }\r
- else\r
- {\r
- sb.append(token);\r
- }\r
- }\r
-\r
- if (removeHTML)\r
- {\r
- sf.description = sb.toString();\r
- }\r
-\r
- }\r
-\r
- /**\r
- * generate a features file for seqs\r
- * \r
- * @param seqs\r
- * source of sequence features\r
- * @param visible\r
- * hash of feature types and colours\r
- * @return features file contents\r
- */\r
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible)\r
- {\r
- return printJalviewFormat(seqs, visible, true);\r
- }\r
-\r
- /**\r
- * generate a features file for seqs with colours from visible (if any)\r
- * \r
- * @param seqs\r
- * source of features\r
- * @param visible\r
- * hash of Colours for each feature type\r
- * @param visOnly\r
- * when true only feature types in 'visible' will be output\r
- * @return features file contents\r
- */\r
- public String printJalviewFormat(SequenceI[] seqs, Hashtable visible,\r
- boolean visOnly)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature[] next;\r
-\r
- if (visOnly && (visible == null || visible.size() < 1))\r
- {\r
- return "No Features Visible";\r
- }\r
- if (visible != null && visOnly)\r
- {\r
- // write feature colours only if we're given them and we are generating\r
- // viewed features\r
- // TODO: decide if feature links should also be written here ?\r
- Enumeration en = visible.keys();\r
- String type, color;\r
- while (en.hasMoreElements())\r
- {\r
- type = en.nextElement().toString();\r
-\r
- if (visible.get(type) instanceof GraduatedColor)\r
- {\r
- GraduatedColor gc = (GraduatedColor) visible.get(type);\r
- color = Format.getHexString(gc.getMinColor()) + "|"\r
- + Format.getHexString(gc.getMaxColor()) +\r
- (gc.isAutoScale() ? "|" : "|abso|")+ gc.getMin() + "|" + gc.getMax() + "|";\r
- if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)\r
- {\r
- if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)\r
- {\r
- color += "below";\r
- }\r
- else\r
- {\r
- if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)\r
- {\r
- System.err.println("WARNING: Unsupported threshold type ("\r
- + gc.getThreshType() + ") : Assuming 'above'");\r
- }\r
- color += "above";\r
- }\r
- // add the value\r
- color += "|" + gc.getThresh();\r
- }\r
- else\r
- {\r
- color += "none";\r
- }\r
- }\r
- else\r
- if (visible.get(type) instanceof java.awt.Color) {\r
- color = Format.getHexString((java.awt.Color)visible.get(type));\r
- } else {\r
- // legacy support for integer objects containing colour triplet values\r
- color = Format.getHexString(new java.awt.Color(Integer\r
- .parseInt(visible.get(type).toString())));\r
- }\r
- out.append(type + "\t" + color + "\n");\r
- }\r
- }\r
- // Work out which groups are both present and visible\r
- Vector groups = new Vector();\r
- int groupIndex = 0;\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- if (next != null)\r
- {\r
- for (int j = 0; j < next.length; j++)\r
- {\r
- if (visOnly && !visible.containsKey(next[j].type))\r
- {\r
- continue;\r
- }\r
-\r
- if (next[j].featureGroup != null\r
- && !groups.contains(next[j].featureGroup))\r
- {\r
- groups.addElement(next[j].featureGroup);\r
- }\r
- }\r
- }\r
- }\r
-\r
- String group = null;\r
-\r
- do\r
- {\r
-\r
- if (groups.size() > 0 && groupIndex < groups.size())\r
- {\r
- group = groups.elementAt(groupIndex).toString();\r
- out.append("\nSTARTGROUP\t" + group + "\n");\r
- }\r
- else\r
- {\r
- group = null;\r
- }\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- if (next != null)\r
- {\r
- for (int j = 0; j < next.length; j++)\r
- {\r
- if (visOnly && !visible.containsKey(next[j].type))\r
- {\r
- continue;\r
- }\r
-\r
- if (group != null\r
- && (next[j].featureGroup == null || !next[j].featureGroup\r
- .equals(group)))\r
- {\r
- continue;\r
- }\r
-\r
- if (group == null && next[j].featureGroup != null)\r
- {\r
- continue;\r
- }\r
-\r
- if (next[j].description == null\r
- || next[j].description.equals(""))\r
- {\r
- out.append(next[j].type + "\t");\r
- }\r
- else\r
- {\r
- if (next[j].links != null\r
- && next[j].getDescription().indexOf("<html>") == -1)\r
- {\r
- out.append("<html>");\r
- }\r
-\r
- out.append(next[j].description + " ");\r
- if (next[j].links != null)\r
- {\r
- for (int l = 0; l < next[j].links.size(); l++)\r
- {\r
- String label = next[j].links.elementAt(l).toString();\r
- String href = label.substring(label.indexOf("|") + 1);\r
- label = label.substring(0, label.indexOf("|"));\r
-\r
- if (next[j].description.indexOf(href) == -1)\r
- {\r
- out\r
- .append("<a href=\"" + href + "\">" + label\r
- + "</a>");\r
- }\r
- }\r
-\r
- if (next[j].getDescription().indexOf("</html>") == -1)\r
- {\r
- out.append("</html>");\r
- }\r
- }\r
-\r
- out.append("\t");\r
- }\r
-\r
- out.append(seqs[i].getName() + "\t-1\t" + next[j].begin + "\t"\r
- + next[j].end + "\t" + next[j].type + ((visible.get(next[j].type) instanceof GraduatedColor) ? "\t"+next[j].score+"\n" : "\n"));\r
- }\r
- }\r
- }\r
-\r
- if (group != null)\r
- {\r
- out.append("ENDGROUP\t" + group + "\n");\r
- groupIndex++;\r
- }\r
- else\r
- {\r
- break;\r
- }\r
-\r
- } while (groupIndex < groups.size() + 1);\r
-\r
- return out.toString();\r
- }\r
-\r
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible)\r
- {\r
- return printGFFFormat(seqs, visible, true);\r
- }\r
-\r
- public String printGFFFormat(SequenceI[] seqs, Hashtable visible,\r
- boolean visOnly)\r
- {\r
- StringBuffer out = new StringBuffer();\r
- SequenceFeature[] next;\r
- String source;\r
-\r
- for (int i = 0; i < seqs.length; i++)\r
- {\r
- if (seqs[i].getSequenceFeatures() != null)\r
- {\r
- next = seqs[i].getSequenceFeatures();\r
- for (int j = 0; j < next.length; j++)\r
- {\r
- if (visOnly && visible != null\r
- && !visible.containsKey(next[j].type))\r
- {\r
- continue;\r
- }\r
-\r
- source = next[j].featureGroup;\r
- if (source == null)\r
- {\r
- source = next[j].getDescription();\r
- }\r
-\r
- out.append(seqs[i].getName() + "\t" + source + "\t"\r
- + next[j].type + "\t" + next[j].begin + "\t"\r
- + next[j].end + "\t" + next[j].score + "\t");\r
-\r
- if (next[j].getValue("STRAND") != null)\r
- {\r
- out.append(next[j].getValue("STRAND") + "\t");\r
- }\r
- else\r
- {\r
- out.append(".\t");\r
- }\r
-\r
- if (next[j].getValue("FRAME") != null)\r
- {\r
- out.append(next[j].getValue("FRAME"));\r
- }\r
- else\r
- {\r
- out.append(".");\r
- }\r
-\r
- if (next[j].getValue("ATTRIBUTES") != null)\r
- {\r
- out.append(next[j].getValue("ATTRIBUTES"));\r
- }\r
-\r
- out.append("\n");\r
-\r
- }\r
- }\r
- }\r
-\r
- return out.toString();\r
- }\r
-\r
- /**\r
- * this is only for the benefit of object polymorphism - method does nothing.\r
- */\r
- public void parse()\r
- {\r
- // IGNORED\r
- }\r
-\r
- /**\r
- * this is only for the benefit of object polymorphism - method does nothing.\r
- * \r
- * @return error message\r
- */\r
- public String print()\r
- {\r
- return "USE printGFFFormat() or printJalviewFormat()";\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.io;
+
+import jalview.analysis.SequenceIdMatcher;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceDummy;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.UserColourScheme;
+import jalview.util.Format;
+import jalview.util.MapList;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+/**
+ * Parse and create Jalview Features files Detects GFF format features files and
+ * parses. Does not implement standard print() - call specific printFeatures or
+ * printGFF. Uses AlignmentI.findSequence(String id) to find the sequence object
+ * for the features annotation - this normally works on an exact match.
+ *
+ * @author AMW
+ * @version $Revision$
+ */
+public class FeaturesFile extends AlignFile
+{
+ /**
+ * work around for GFF interpretation bug where source string becomes
+ * description rather than a group
+ */
+ private boolean doGffSource = true;
+
+ private int gffversion;
+
+ /**
+ * Creates a new FeaturesFile object.
+ */
+ public FeaturesFile()
+ {
+ }
+
+ /**
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(String inFile, String type) throws IOException
+ {
+ super(inFile, type);
+ }
+
+ /**
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(FileParse source) throws IOException
+ {
+ super(source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param source
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, FileParse source)
+ throws IOException
+ {
+ super(parseImmediately, source);
+ }
+
+ /**
+ * @param parseImmediately
+ * @param inFile
+ * @param type
+ * @throws IOException
+ */
+ public FeaturesFile(boolean parseImmediately, String inFile, String type)
+ throws IOException
+ {
+ super(parseImmediately, inFile, type);
+ }
+
+ /**
+ * Parse GFF or sequence features file using case-independent matching,
+ * discarding URLs
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param removeHTML
+ * - process html strings into plain text
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML)
+ {
+ return parse(align, colours, null, removeHTML, false);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally using case-independent
+ * matching, discarding URLs
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param removeHTML
+ * - process html strings into plain text
+ * @param relaxedIdmatching
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, boolean removeHTML,
+ boolean relaxedIdMatching)
+ {
+ return parse(align, colours, null, removeHTML, relaxedIdMatching);
+ }
+
+ /**
+ * Parse GFF or sequence features file optionally using case-independent
+ * matching
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param featureLink
+ * - hashtable to store associated URLs
+ * @param removeHTML
+ * - process html strings into plain text
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, Map featureLink,
+ boolean removeHTML)
+ {
+ return parse(align, colours, featureLink, removeHTML, false);
+ }
+
+ @Override
+ public void addAnnotations(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addAnnotations(al);
+ }
+
+ @Override
+ public void addProperties(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addProperties(al);
+ }
+
+ @Override
+ public void addSeqGroups(AlignmentI al)
+ {
+ // TODO Auto-generated method stub
+ super.addSeqGroups(al);
+ }
+
+ /**
+ * Parse GFF or sequence features file
+ *
+ * @param align
+ * - alignment/dataset containing sequences that are to be annotated
+ * @param colours
+ * - hashtable to store feature colour definitions
+ * @param featureLink
+ * - hashtable to store associated URLs
+ * @param removeHTML
+ * - process html strings into plain text
+ * @param relaxedIdmatching
+ * - when true, ID matches to compound sequence IDs are allowed
+ * @return true if features were added
+ */
+ public boolean parse(AlignmentI align, Map colours, Map featureLink,
+ boolean removeHTML, boolean relaxedIdmatching)
+ {
+
+ String line = null;
+ try
+ {
+ SequenceI seq = null;
+ /**
+ * keep track of any sequences we try to create from the data if it is a
+ * GFF3 file
+ */
+ ArrayList<SequenceI> newseqs = new ArrayList<SequenceI>();
+ String type, desc, token = null;
+
+ int index, start, end;
+ float score;
+ StringTokenizer st;
+ SequenceFeature sf;
+ String featureGroup = null, groupLink = null;
+ Map typeLink = new Hashtable();
+ /**
+ * when true, assume GFF style features rather than Jalview style.
+ */
+ boolean GFFFile = true;
+ Map<String, String> gffProps = new HashMap<String, String>();
+ while ((line = nextLine()) != null)
+ {
+ // skip comments/process pragmas
+ if (line.startsWith("#"))
+ {
+ if (line.startsWith("##"))
+ {
+ // possibly GFF2/3 version and metadata header
+ processGffPragma(line, gffProps, align, newseqs);
+ line = "";
+ }
+ continue;
+ }
+
+ st = new StringTokenizer(line, "\t");
+ if (st.countTokens() == 1)
+ {
+ if (line.trim().equalsIgnoreCase("GFF"))
+ {
+ // Start parsing file as if it might be GFF again.
+ GFFFile = true;
+ continue;
+ }
+ }
+ if (st.countTokens() > 1 && st.countTokens() < 4)
+ {
+ GFFFile = false;
+ type = st.nextToken();
+ if (type.equalsIgnoreCase("startgroup"))
+ {
+ featureGroup = st.nextToken();
+ if (st.hasMoreElements())
+ {
+ groupLink = st.nextToken();
+ featureLink.put(featureGroup, groupLink);
+ }
+ }
+ else if (type.equalsIgnoreCase("endgroup"))
+ {
+ // We should check whether this is the current group,
+ // but at present theres no way of showing more than 1 group
+ st.nextToken();
+ featureGroup = null;
+ groupLink = null;
+ }
+ else
+ {
+ Object colour = null;
+ String colscheme = st.nextToken();
+ if (colscheme.indexOf("|") > -1
+ || colscheme.trim().equalsIgnoreCase("label"))
+ {
+ // Parse '|' separated graduated colourscheme fields:
+ // [label|][mincolour|maxcolour|[absolute|]minvalue|maxvalue|thresholdtype|thresholdvalue]
+ // can either provide 'label' only, first is optional, next two
+ // colors are required (but may be
+ // left blank), next is optional, nxt two min/max are required.
+ // first is either 'label'
+ // first/second and third are both hexadecimal or word equivalent
+ // colour.
+ // next two are values parsed as floats.
+ // fifth is either 'above','below', or 'none'.
+ // sixth is a float value and only required when fifth is either
+ // 'above' or 'below'.
+ StringTokenizer gcol = new StringTokenizer(colscheme, "|",
+ true);
+ // set defaults
+ int threshtype = AnnotationColourGradient.NO_THRESHOLD;
+ float min = Float.MIN_VALUE, max = Float.MAX_VALUE, threshval = Float.NaN;
+ boolean labelCol = false;
+ // Parse spec line
+ String mincol = gcol.nextToken();
+ if (mincol == "|")
+ {
+ System.err
+ .println("Expected either 'label' or a colour specification in the line: "
+ + line);
+ continue;
+ }
+ String maxcol = null;
+ if (mincol.toLowerCase().indexOf("label") == 0)
+ {
+ labelCol = true;
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null); // skip
+ // '|'
+ mincol = (gcol.hasMoreTokens() ? gcol.nextToken() : null);
+ }
+ String abso = null, minval, maxval;
+ if (mincol != null)
+ {
+ // at least four more tokens
+ if (mincol.equals("|"))
+ {
+ mincol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ // continue parsing rest of line
+ maxcol = gcol.nextToken();
+ if (maxcol.equals("|"))
+ {
+ maxcol = "";
+ }
+ else
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ abso = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ if (abso.toLowerCase().indexOf("abso") != 0)
+ {
+ minval = abso;
+ abso = null;
+ }
+ else
+ {
+ minval = gcol.nextToken();
+ gcol.nextToken(); // skip next '|'
+ }
+ maxval = gcol.nextToken();
+ if (gcol.hasMoreTokens())
+ {
+ gcol.nextToken(); // skip next '|'
+ }
+ try
+ {
+ if (minval.length() > 0)
+ {
+ min = new Float(minval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the minimum value for graduated colour for type ("
+ + colscheme
+ + ") - did you misspell 'auto' for the optional automatic colour switch ?");
+ e.printStackTrace();
+ }
+ try
+ {
+ if (maxval.length() > 0)
+ {
+ max = new Float(maxval).floatValue();
+ }
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the maximum value for graduated colour for type ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ }
+ else
+ {
+ // add in some dummy min/max colours for the label-only
+ // colourscheme.
+ mincol = "FFFFFF";
+ maxcol = "000000";
+ }
+ try
+ {
+ colour = new jalview.schemes.GraduatedColor(
+ new UserColourScheme(mincol).findColour('A'),
+ new UserColourScheme(maxcol).findColour('A'), min,
+ max);
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse the graduated colour scheme ("
+ + colscheme + ")");
+ e.printStackTrace();
+ }
+ if (colour != null)
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setColourByLabel(labelCol);
+ ((jalview.schemes.GraduatedColor) colour)
+ .setAutoScaled(abso == null);
+ // add in any additional parameters
+ String ttype = null, tval = null;
+ if (gcol.hasMoreTokens())
+ {
+ // threshold type and possibly a threshold value
+ ttype = gcol.nextToken();
+ if (ttype.toLowerCase().startsWith("below"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.BELOW_THRESHOLD);
+ }
+ else if (ttype.toLowerCase().startsWith("above"))
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.ABOVE_THRESHOLD);
+ }
+ else
+ {
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThreshType(AnnotationColourGradient.NO_THRESHOLD);
+ if (!ttype.toLowerCase().startsWith("no"))
+ {
+ System.err
+ .println("Ignoring unrecognised threshold type : "
+ + ttype);
+ }
+ }
+ }
+ if (((GraduatedColor) colour).getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ try
+ {
+ gcol.nextToken();
+ tval = gcol.nextToken();
+ ((jalview.schemes.GraduatedColor) colour)
+ .setThresh(new Float(tval).floatValue());
+ } catch (Exception e)
+ {
+ System.err
+ .println("Couldn't parse threshold value as a float: ("
+ + tval + ")");
+ e.printStackTrace();
+ }
+ }
+ // parse the thresh-is-min token ?
+ if (gcol.hasMoreTokens())
+ {
+ System.err
+ .println("Ignoring additional tokens in parameters in graduated colour specification\n");
+ while (gcol.hasMoreTokens())
+ {
+ System.err.println("|" + gcol.nextToken());
+ }
+ System.err.println("\n");
+ }
+ }
+ }
+ else
+ {
+ UserColourScheme ucs = new UserColourScheme(colscheme);
+ colour = ucs.findColour('A');
+ }
+ if (colour != null)
+ {
+ colours.put(type, colour);
+ }
+ if (st.hasMoreElements())
+ {
+ String link = st.nextToken();
+ typeLink.put(type, link);
+ if (featureLink == null)
+ {
+ featureLink = new Hashtable();
+ }
+ featureLink.put(type, link);
+ }
+ }
+ continue;
+ }
+ String seqId = "";
+ while (st.hasMoreElements())
+ {
+
+ if (GFFFile)
+ {
+ // Still possible this is an old Jalview file,
+ // which does not have type colours at the beginning
+ seqId = token = st.nextToken();
+ seq = findName(align, seqId, relaxedIdmatching, newseqs);
+ if (seq != null)
+ {
+ desc = st.nextToken();
+ String group = null;
+ if (doGffSource && desc.indexOf(' ') == -1)
+ {
+ // could also be a source term rather than description line
+ group = new String(desc);
+ }
+ type = st.nextToken();
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ start = 0;
+ }
+ else
+ {
+ start = Integer.parseInt(stt);
+ }
+ } catch (NumberFormatException ex)
+ {
+ start = 0;
+ }
+ try
+ {
+ String stt = st.nextToken();
+ if (stt.length() == 0 || stt.equals("-"))
+ {
+ end = 0;
+ }
+ else
+ {
+ end = Integer.parseInt(stt);
+ }
+ } catch (NumberFormatException ex)
+ {
+ end = 0;
+ }
+ // TODO: decide if non positional feature assertion for input data
+ // where end==0 is generally valid
+ if (end == 0)
+ {
+ // treat as non-positional feature, regardless.
+ start = 0;
+ }
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ } catch (NumberFormatException ex)
+ {
+ score = 0;
+ }
+
+ sf = new SequenceFeature(type, desc, start, end, score, group);
+
+ try
+ {
+ sf.setValue("STRAND", st.nextToken());
+ sf.setValue("FRAME", st.nextToken());
+ } catch (Exception ex)
+ {
+ }
+
+ if (st.hasMoreTokens())
+ {
+ StringBuffer attributes = new StringBuffer();
+ boolean sep = false;
+ while (st.hasMoreTokens())
+ {
+ attributes.append((sep ? "\t" : "") + st.nextElement());
+ sep = true;
+ }
+ // TODO validate and split GFF2 attributes field ? parse out
+ // ([A-Za-z][A-Za-z0-9_]*) <value> ; and add as
+ // sf.setValue(attrib, val);
+ sf.setValue("ATTRIBUTES", attributes.toString());
+ }
+
+ if (processOrAddSeqFeature(align, newseqs, seq, sf, GFFFile,
+ relaxedIdmatching))
+ {
+ // check whether we should add the sequence feature to any other
+ // sequences in the alignment with the same or similar
+ while ((seq = align.findName(seq, seqId, true)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ }
+ break;
+ }
+ }
+
+ if (GFFFile && seq == null)
+ {
+ desc = token;
+ }
+ else
+ {
+ desc = st.nextToken();
+ }
+ if (!st.hasMoreTokens())
+ {
+ System.err
+ .println("DEBUG: Run out of tokens when trying to identify the destination for the feature.. giving up.");
+ // in all probability, this isn't a file we understand, so bail
+ // quietly.
+ return false;
+ }
+
+ token = st.nextToken();
+
+ if (!token.equals("ID_NOT_SPECIFIED"))
+ {
+ seq = findName(align, seqId = token, relaxedIdmatching, null);
+ st.nextToken();
+ }
+ else
+ {
+ seqId = null;
+ try
+ {
+ index = Integer.parseInt(st.nextToken());
+ seq = align.getSequenceAt(index);
+ } catch (NumberFormatException ex)
+ {
+ seq = null;
+ }
+ }
+
+ if (seq == null)
+ {
+ System.out.println("Sequence not found: " + line);
+ break;
+ }
+
+ start = Integer.parseInt(st.nextToken());
+ end = Integer.parseInt(st.nextToken());
+
+ type = st.nextToken();
+
+ if (!colours.containsKey(type))
+ {
+ // Probably the old style groups file
+ UserColourScheme ucs = new UserColourScheme(type);
+ colours.put(type, ucs.findColour('A'));
+ }
+ sf = new SequenceFeature(type, desc, "", start, end, featureGroup);
+ if (st.hasMoreTokens())
+ {
+ try
+ {
+ score = new Float(st.nextToken()).floatValue();
+ // update colourgradient bounds if allowed to
+ } catch (NumberFormatException ex)
+ {
+ score = 0;
+ }
+ sf.setScore(score);
+ }
+ if (groupLink != null && removeHTML)
+ {
+ sf.addLink(groupLink);
+ sf.description += "%LINK%";
+ }
+ if (typeLink.containsKey(type) && removeHTML)
+ {
+ sf.addLink(typeLink.get(type).toString());
+ sf.description += "%LINK%";
+ }
+
+ parseDescriptionHTML(sf, removeHTML);
+
+ seq.addSequenceFeature(sf);
+
+ while (seqId != null
+ && (seq = align.findName(seq, seqId, false)) != null)
+ {
+ seq.addSequenceFeature(new SequenceFeature(sf));
+ }
+ // If we got here, its not a GFFFile
+ GFFFile = false;
+ }
+ }
+ resetMatcher();
+ } catch (Exception ex)
+ {
+ // should report somewhere useful for UI if necessary
+ warningMessage = ((warningMessage == null) ? "" : warningMessage)
+ + "Parsing error at\n" + line;
+ System.out.println("Error parsing feature file: " + ex + "\n" + line);
+ ex.printStackTrace(System.err);
+ resetMatcher();
+ return false;
+ }
+
+ return true;
+ }
+
+ private enum GffPragmas
+ {
+ gff_version, sequence_region, feature_ontology, attribute_ontology, source_ontology, species_build, fasta, hash
+ };
+
+ private static Map<String, GffPragmas> GFFPRAGMA;
+ static
+ {
+ GFFPRAGMA = new HashMap<String, GffPragmas>();
+ GFFPRAGMA.put("sequence-region", GffPragmas.sequence_region);
+ GFFPRAGMA.put("feature-ontology", GffPragmas.feature_ontology);
+ GFFPRAGMA.put("#", GffPragmas.hash);
+ GFFPRAGMA.put("fasta", GffPragmas.fasta);
+ GFFPRAGMA.put("species-build", GffPragmas.species_build);
+ GFFPRAGMA.put("source-ontology", GffPragmas.source_ontology);
+ GFFPRAGMA.put("attribute-ontology", GffPragmas.attribute_ontology);
+ }
+
+ private void processGffPragma(String line, Map<String, String> gffProps,
+ AlignmentI align, ArrayList<SequenceI> newseqs)
+ throws IOException
+ {
+ // line starts with ##
+ int spacepos = line.indexOf(' ');
+ String pragma = spacepos == -1 ? line.substring(2).trim() : line
+ .substring(2, spacepos);
+ GffPragmas gffpragma = GFFPRAGMA.get(pragma.toLowerCase());
+ if (gffpragma == null)
+ {
+ return;
+ }
+ switch (gffpragma)
+ {
+ case gff_version:
+ try
+ {
+ gffversion = Integer.parseInt(line.substring(spacepos + 1));
+ } finally
+ {
+
+ }
+ break;
+ case feature_ontology:
+ // resolve against specific feature ontology
+ break;
+ case attribute_ontology:
+ // resolve against specific attribute ontology
+ break;
+ case source_ontology:
+ // resolve against specific source ontology
+ break;
+ case species_build:
+ // resolve against specific NCBI taxon version
+ break;
+ case hash:
+ // close off any open feature hierarchies
+ break;
+ case fasta:
+ // process the rest of the file as a fasta file and replace any dummy
+ // sequence IDs
+ process_as_fasta(align, newseqs);
+ break;
+ default:
+ // we do nothing ?
+ System.err.println("Ignoring unknown pragma:\n" + line);
+ }
+ }
+
+ private void process_as_fasta(AlignmentI align, List<SequenceI> newseqs)
+ throws IOException
+ {
+ try
+ {
+ mark();
+ } catch (IOException q)
+ {
+ }
+ FastaFile parser = new FastaFile(this);
+ List<SequenceI> includedseqs = parser.getSeqs();
+ SequenceIdMatcher smatcher = new SequenceIdMatcher(newseqs);
+ // iterate over includedseqs, and replacing matching ones with newseqs
+ // sequences. Generic iterator not used here because we modify includedseqs
+ // as we go
+ for (int p = 0, pSize = includedseqs.size(); p < pSize; p++)
+ {
+ // search for any dummy seqs that this sequence can be used to update
+ SequenceI dummyseq = smatcher.findIdMatch(includedseqs.get(p));
+ if (dummyseq != null)
+ {
+ // dummyseq was created so it could be annotated and referred to in
+ // alignments/codon mappings
+
+ SequenceI mseq = includedseqs.get(p);
+ // mseq is the 'template' imported from the FASTA file which we'll use
+ // to coomplete dummyseq
+ if (dummyseq instanceof SequenceDummy)
+ {
+ // probably have the pattern wrong
+ // idea is that a flyweight proxy for a sequence ID can be created for
+ // 1. stable reference creation
+ // 2. addition of annotation
+ // 3. future replacement by a real sequence
+ // current pattern is to create SequenceDummy objects - a convenience
+ // constructor for a Sequence.
+ // problem is that when promoted to a real sequence, all references
+ // need
+ // to be updated somehow.
+ ((SequenceDummy) dummyseq).become(mseq);
+ includedseqs.set(p, dummyseq); // template is no longer needed
+ }
+ }
+ }
+ // finally add sequences to the dataset
+ for (SequenceI seq : includedseqs)
+ {
+ align.addSequence(seq);
+ }
+ }
+
+ /**
+ * take a sequence feature and examine its attributes to decide how it should
+ * be added to a sequence
+ *
+ * @param seq
+ * - the destination sequence constructed or discovered in the
+ * current context
+ * @param sf
+ * - the base feature with ATTRIBUTES property containing any
+ * additional attributes
+ * @param gFFFile
+ * - true if we are processing a GFF annotation file
+ * @return true if sf was actually added to the sequence, false if it was
+ * processed in another way
+ */
+ public boolean processOrAddSeqFeature(AlignmentI align,
+ List<SequenceI> newseqs, SequenceI seq, SequenceFeature sf,
+ boolean gFFFile, boolean relaxedIdMatching)
+ {
+ String attr = (String) sf.getValue("ATTRIBUTES");
+ boolean add = true;
+ if (gFFFile && attr != null)
+ {
+ int nattr = 8;
+
+ for (String attset : attr.split("\t"))
+ {
+ if (attset == null || attset.trim().length() == 0)
+ {
+ continue;
+ }
+ nattr++;
+ Map<String, List<String>> set = new HashMap<String, List<String>>();
+ // normally, only expect one column - 9 - in this field
+ // the attributes (Gff3) or groups (gff2) field
+ for (String pair : attset.trim().split(";"))
+ {
+ pair = pair.trim();
+ if (pair.length() == 0)
+ {
+ continue;
+ }
+
+ // expect either space seperated (gff2) or '=' separated (gff3)
+ // key/value pairs here
+
+ int eqpos = pair.indexOf('='), sppos = pair.indexOf(' ');
+ String key = null, value = null;
+
+ if (sppos > -1 && (eqpos == -1 || sppos < eqpos))
+ {
+ key = pair.substring(0, sppos);
+ value = pair.substring(sppos + 1);
+ }
+ else
+ {
+ if (eqpos > -1 && (sppos == -1 || eqpos < sppos))
+ {
+ key = pair.substring(0, eqpos);
+ value = pair.substring(eqpos + 1);
+ }
+ else
+ {
+ key = pair;
+ }
+ }
+ if (key != null)
+ {
+ List<String> vals = set.get(key);
+ if (vals == null)
+ {
+ vals = new ArrayList<String>();
+ set.put(key, vals);
+ }
+ if (value != null)
+ {
+ vals.add(value.trim());
+ }
+ }
+ }
+ try
+ {
+ add &= processGffKey(set, nattr, seq, sf, align, newseqs,
+ relaxedIdMatching); // process decides if
+ // feature is actually
+ // added
+ } catch (InvalidGFF3FieldException ivfe)
+ {
+ System.err.println(ivfe);
+ }
+ }
+ }
+ if (add)
+ {
+ seq.addSequenceFeature(sf);
+ }
+ return add;
+ }
+
+ public class InvalidGFF3FieldException extends Exception
+ {
+ String field, value;
+
+ public InvalidGFF3FieldException(String field,
+ Map<String, List<String>> set, String message)
+ {
+ super(message + " (Field was " + field + " and value was "
+ + set.get(field).toString());
+ this.field = field;
+ this.value = set.get(field).toString();
+ }
+
+ }
+
+ /**
+ * take a set of keys for a feature and interpret them
+ *
+ * @param set
+ * @param nattr
+ * @param seq
+ * @param sf
+ * @return
+ */
+ public boolean processGffKey(Map<String, List<String>> set, int nattr,
+ SequenceI seq, SequenceFeature sf, AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching)
+ throws InvalidGFF3FieldException
+ {
+ String attr;
+ // decide how to interpret according to type
+ if (sf.getType().equals("similarity"))
+ {
+ int strand = sf.getStrand();
+ // exonerate cdna/protein map
+ // look for fields
+ List<SequenceI> querySeq = findNames(align, newseqs,
+ relaxedIdMatching, set.get(attr = "Query"));
+ if (querySeq == null || querySeq.size() != 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Expecting exactly one sequence in Query field (got "
+ + set.get(attr) + ")");
+ }
+ if (set.containsKey(attr = "Align"))
+ {
+ // process the align maps and create cdna/protein maps
+ // ideally, the query sequences are in the alignment, but maybe not...
+
+ AlignedCodonFrame alco = new AlignedCodonFrame();
+ MapList codonmapping = constructCodonMappingFromAlign(set, attr,
+ strand);
+
+ // add codon mapping, and hope!
+ alco.addMap(seq, querySeq.get(0), codonmapping);
+ align.addCodonFrame(alco);
+ // everything that's needed to be done is done
+ // no features to create here !
+ return false;
+ }
+
+ }
+ return true;
+ }
+
+ private MapList constructCodonMappingFromAlign(
+ Map<String, List<String>> set, String attr, int strand)
+ throws InvalidGFF3FieldException
+ {
+ if (strand == 0)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid strand for a codon mapping (cannot be 0)");
+ }
+ List<Integer> fromrange = new ArrayList<Integer>(), torange = new ArrayList<Integer>();
+ int lastppos = 0, lastpframe = 0;
+ for (String range : set.get(attr))
+ {
+ List<Integer> ints = new ArrayList<Integer>();
+ StringTokenizer st = new StringTokenizer(range, " ");
+ while (st.hasMoreTokens())
+ {
+ String num = st.nextToken();
+ try
+ {
+ ints.add(new Integer(num));
+ } catch (NumberFormatException nfe)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number in field " + num);
+ }
+ }
+ // Align positionInRef positionInQuery LengthInRef
+ // contig_1146 exonerate:protein2genome:local similarity 8534 11269
+ // 3652 - . alignment_id 0 ;
+ // Query DDB_G0269124
+ // Align 11270 143 120
+ // corresponds to : 120 bases align at pos 143 in protein to 11270 on
+ // dna in strand direction
+ // Align 11150 187 282
+ // corresponds to : 282 bases align at pos 187 in protein to 11150 on
+ // dna in strand direction
+ //
+ // Align 10865 281 888
+ // Align 9977 578 1068
+ // Align 8909 935 375
+ //
+ if (ints.size() != 3)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Invalid number of fields for this attribute ("
+ + ints.size() + ")");
+ }
+ fromrange.add(new Integer(ints.get(0).intValue()));
+ fromrange.add(new Integer(ints.get(0).intValue() + strand
+ * ints.get(2).intValue()));
+ // how are intron/exon boundaries that do not align in codons
+ // represented
+ if (ints.get(1).equals(lastppos) && lastpframe > 0)
+ {
+ // extend existing to map
+ lastppos += ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.set(torange.size() - 1, new Integer(lastppos));
+ }
+ else
+ {
+ // new to map range
+ torange.add(ints.get(1));
+ lastppos = ints.get(1) + ints.get(2) / 3;
+ lastpframe = ints.get(2) % 3;
+ torange.add(new Integer(lastppos));
+ }
+ }
+ // from and to ranges must end up being a series of start/end intervals
+ if (fromrange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the DNA alignment range correctly");
+ }
+ if (torange.size() % 2 == 1)
+ {
+ throw new InvalidGFF3FieldException(attr, set,
+ "Couldn't parse the protein alignment range correctly");
+ }
+ // finally, build the map
+ int[] frommap = new int[fromrange.size()], tomap = new int[torange
+ .size()];
+ int p = 0;
+ for (Integer ip : fromrange)
+ {
+ frommap[p++] = ip.intValue();
+ }
+ p = 0;
+ for (Integer ip : torange)
+ {
+ tomap[p++] = ip.intValue();
+ }
+
+ return new MapList(frommap, tomap, 3, 1);
+ }
+
+ private List<SequenceI> findNames(AlignmentI align,
+ List<SequenceI> newseqs, boolean relaxedIdMatching,
+ List<String> list)
+ {
+ List<SequenceI> found = new ArrayList<SequenceI>();
+ for (String seqId : list)
+ {
+ SequenceI seq = findName(align, seqId, relaxedIdMatching, newseqs);
+ if (seq != null)
+ {
+ found.add(seq);
+ }
+ }
+ return found;
+ }
+
+ private AlignmentI lastmatchedAl = null;
+
+ private SequenceIdMatcher matcher = null;
+
+ /**
+ * clear any temporary handles used to speed up ID matching
+ */
+ private void resetMatcher()
+ {
+ lastmatchedAl = null;
+ matcher = null;
+ }
+
+ private SequenceI findName(AlignmentI align, String seqId,
+ boolean relaxedIdMatching, List<SequenceI> newseqs)
+ {
+ SequenceI match = null;
+ if (relaxedIdMatching)
+ {
+ if (lastmatchedAl != align)
+ {
+ matcher = new SequenceIdMatcher(
+ (lastmatchedAl = align).getSequencesArray());
+ if (newseqs != null)
+ {
+ matcher.addAll(newseqs);
+ }
+ }
+ match = matcher.findIdMatch(seqId);
+ }
+ else
+ {
+ match = align.findName(seqId, true);
+ if (match == null && newseqs != null)
+ {
+ for (SequenceI m : newseqs)
+ {
+ if (seqId.equals(m.getName()))
+ {
+ return m;
+ }
+ }
+ }
+
+ }
+ if (match == null && newseqs != null)
+ {
+ match = new SequenceDummy(seqId);
+ if (relaxedIdMatching)
+ {
+ matcher.addAll(Arrays.asList(new SequenceI[] { match }));
+ }
+ // add dummy sequence to the newseqs list
+ newseqs.add(match);
+ }
+ return match;
+ }
+
+ public void parseDescriptionHTML(SequenceFeature sf, boolean removeHTML)
+ {
+ if (sf.getDescription() == null)
+ {
+ return;
+ }
+ jalview.util.ParseHtmlBodyAndLinks parsed = new jalview.util.ParseHtmlBodyAndLinks(
+ sf.getDescription(), removeHTML, newline);
+
+ sf.description = (removeHTML) ? parsed.getNonHtmlContent()
+ : sf.description;
+ for (String link : parsed.getLinks())
+ {
+ sf.addLink(link);
+ }
+
+ }
+
+ /**
+ * generate a features file for seqs includes non-pos features by default.
+ *
+ * @param seqs
+ * source of sequence features
+ * @param visible
+ * hash of feature types and colours
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] seqs,
+ Map<String, Object> visible)
+ {
+ return printJalviewFormat(seqs, visible, true, true);
+ }
+
+ /**
+ * generate a features file for seqs with colours from visible (if any)
+ *
+ * @param seqs
+ * source of features
+ * @param visible
+ * hash of Colours for each feature type
+ * @param visOnly
+ * when true only feature types in 'visible' will be output
+ * @param nonpos
+ * indicates if non-positional features should be output (regardless
+ * of group or type)
+ * @return features file contents
+ */
+ public String printJalviewFormat(SequenceI[] seqs, Map visible,
+ boolean visOnly, boolean nonpos)
+ {
+ StringBuffer out = new StringBuffer();
+ SequenceFeature[] next;
+ boolean featuresGen = false;
+ if (visOnly && !nonpos && (visible == null || visible.size() < 1))
+ {
+ // no point continuing.
+ return "No Features Visible";
+ }
+
+ if (visible != null && visOnly)
+ {
+ // write feature colours only if we're given them and we are generating
+ // viewed features
+ // TODO: decide if feature links should also be written here ?
+ Iterator en = visible.keySet().iterator();
+ String type, color;
+ while (en.hasNext())
+ {
+ type = en.next().toString();
+
+ if (visible.get(type) instanceof GraduatedColor)
+ {
+ GraduatedColor gc = (GraduatedColor) visible.get(type);
+ color = (gc.isColourByLabel() ? "label|" : "")
+ + Format.getHexString(gc.getMinColor()) + "|"
+ + Format.getHexString(gc.getMaxColor())
+ + (gc.isAutoScale() ? "|" : "|abso|") + gc.getMin() + "|"
+ + gc.getMax() + "|";
+ if (gc.getThreshType() != AnnotationColourGradient.NO_THRESHOLD)
+ {
+ if (gc.getThreshType() == AnnotationColourGradient.BELOW_THRESHOLD)
+ {
+ color += "below";
+ }
+ else
+ {
+ if (gc.getThreshType() != AnnotationColourGradient.ABOVE_THRESHOLD)
+ {
+ System.err.println("WARNING: Unsupported threshold type ("
+ + gc.getThreshType() + ") : Assuming 'above'");
+ }
+ color += "above";
+ }
+ // add the value
+ color += "|" + gc.getThresh();
+ }
+ else
+ {
+ color += "none";
+ }
+ }
+ else if (visible.get(type) instanceof java.awt.Color)
+ {
+ color = Format.getHexString((java.awt.Color) visible.get(type));
+ }
+ else
+ {
+ // legacy support for integer objects containing colour triplet values
+ color = Format.getHexString(new java.awt.Color(Integer
+ .parseInt(visible.get(type).toString())));
+ }
+ out.append(type);
+ out.append("\t");
+ out.append(color);
+ out.append(newline);
+ }
+ }
+ // Work out which groups are both present and visible
+ Vector groups = new Vector();
+ int groupIndex = 0;
+ boolean isnonpos = false;
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ next = seqs[i].getSequenceFeatures();
+ if (next != null)
+ {
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ continue;
+ }
+
+ if (next[j].featureGroup != null
+ && !groups.contains(next[j].featureGroup))
+ {
+ groups.addElement(next[j].featureGroup);
+ }
+ }
+ }
+ }
+
+ String group = null;
+ do
+ {
+
+ if (groups.size() > 0 && groupIndex < groups.size())
+ {
+ group = groups.elementAt(groupIndex).toString();
+ out.append(newline);
+ out.append("STARTGROUP\t");
+ out.append(group);
+ out.append(newline);
+ }
+ else
+ {
+ group = null;
+ }
+
+ for (int i = 0; i < seqs.length; i++)
+ {
+ next = seqs[i].getSequenceFeatures();
+ if (next != null)
+ {
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ // skip if feature is nonpos and we ignore them or if we only
+ // output visible and it isn't non-pos and it's not visible
+ continue;
+ }
+
+ if (group != null
+ && (next[j].featureGroup == null || !next[j].featureGroup
+ .equals(group)))
+ {
+ continue;
+ }
+
+ if (group == null && next[j].featureGroup != null)
+ {
+ continue;
+ }
+ // we have features to output
+ featuresGen = true;
+ if (next[j].description == null
+ || next[j].description.equals(""))
+ {
+ out.append(next[j].type + "\t");
+ }
+ else
+ {
+ if (next[j].links != null
+ && next[j].getDescription().indexOf("<html>") == -1)
+ {
+ out.append("<html>");
+ }
+
+ out.append(next[j].description + " ");
+ if (next[j].links != null)
+ {
+ for (int l = 0; l < next[j].links.size(); l++)
+ {
+ String label = next[j].links.elementAt(l).toString();
+ String href = label.substring(label.indexOf("|") + 1);
+ label = label.substring(0, label.indexOf("|"));
+
+ if (next[j].description.indexOf(href) == -1)
+ {
+ out.append("<a href=\"" + href + "\">" + label + "</a>");
+ }
+ }
+
+ if (next[j].getDescription().indexOf("</html>") == -1)
+ {
+ out.append("</html>");
+ }
+ }
+
+ out.append("\t");
+ }
+ out.append(seqs[i].getName());
+ out.append("\t-1\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].type);
+ if (!Float.isNaN(next[j].score))
+ {
+ out.append("\t");
+ out.append(next[j].score);
+ }
+ out.append(newline);
+ }
+ }
+ }
+
+ if (group != null)
+ {
+ out.append("ENDGROUP\t");
+ out.append(group);
+ out.append(newline);
+ groupIndex++;
+ }
+ else
+ {
+ break;
+ }
+
+ } while (groupIndex < groups.size() + 1);
+
+ if (!featuresGen)
+ {
+ return "No Features Visible";
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * generate a gff file for sequence features includes non-pos features by
+ * default.
+ *
+ * @param seqs
+ * @param visible
+ * @return
+ */
+ public String printGFFFormat(SequenceI[] seqs, Map<String, Object> visible)
+ {
+ return printGFFFormat(seqs, visible, true, true);
+ }
+
+ public String printGFFFormat(SequenceI[] seqs,
+ Map<String, Object> visible, boolean visOnly, boolean nonpos)
+ {
+ StringBuffer out = new StringBuffer();
+ SequenceFeature[] next;
+ String source;
+ boolean isnonpos;
+ for (int i = 0; i < seqs.length; i++)
+ {
+ if (seqs[i].getSequenceFeatures() != null)
+ {
+ next = seqs[i].getSequenceFeatures();
+ for (int j = 0; j < next.length; j++)
+ {
+ isnonpos = next[j].begin == 0 && next[j].end == 0;
+ if ((!nonpos && isnonpos)
+ || (!isnonpos && visOnly && !visible
+ .containsKey(next[j].type)))
+ {
+ continue;
+ }
+
+ source = next[j].featureGroup;
+ if (source == null)
+ {
+ source = next[j].getDescription();
+ }
+
+ out.append(seqs[i].getName());
+ out.append("\t");
+ out.append(source);
+ out.append("\t");
+ out.append(next[j].type);
+ out.append("\t");
+ out.append(next[j].begin);
+ out.append("\t");
+ out.append(next[j].end);
+ out.append("\t");
+ out.append(next[j].score);
+ out.append("\t");
+
+ if (next[j].getValue("STRAND") != null)
+ {
+ out.append(next[j].getValue("STRAND"));
+ out.append("\t");
+ }
+ else
+ {
+ out.append(".\t");
+ }
+
+ if (next[j].getValue("FRAME") != null)
+ {
+ out.append(next[j].getValue("FRAME"));
+ }
+ else
+ {
+ out.append(".");
+ }
+ // TODO: verify/check GFF - should there be a /t here before attribute
+ // output ?
+
+ if (next[j].getValue("ATTRIBUTES") != null)
+ {
+ out.append(next[j].getValue("ATTRIBUTES"));
+ }
+
+ out.append(newline);
+
+ }
+ }
+ }
+
+ return out.toString();
+ }
+
+ /**
+ * this is only for the benefit of object polymorphism - method does nothing.
+ */
+ public void parse()
+ {
+ // IGNORED
+ }
+
+ /**
+ * this is only for the benefit of object polymorphism - method does nothing.
+ *
+ * @return error message
+ */
+ public String print()
+ {
+ return "USE printGFFFormat() or printJalviewFormat()";
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff